Contact

Description

PHAST is a freely available software package for comparative and
evolutionary genomics. It consists of about half a dozen major
programs, plus more than a dozen utilities for
manipulating sequence alignments, phylogenetic trees, and genomic
annotations (see left panel). For the most part, PHAST focuses on two
kinds of applications: the identification of novel functional
elements, including protein-coding exons and evolutionarily conserved
sequences; and statistical phylogenetic modeling, including estimation of
model parameters, detection of signatures of selection, and reconstruction
of ancestral sequences. It consists of
over 60,000 lines of C code.

PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison).

RPHAST

Many phast functions can now be accessed from within the R
environment using the rphast package. It is available from
the RPHAST webpage and
also on CRAN.

Platforms and Dependencies

PHAST is written in standard C and should compile cleanly on any
standard UNIX platform (including Mac OS X). PHAST is mostly
self-contained, but
it does depend on the LAPACK
package for certain
matrix operations (diagonalization and inversion). On Mac OS X (version
10.3 or later) LAPACK is built-in, but on other platforms, the C port of
LAPACK, called CLAPACK,
must
be installed for PHAST to be fully functional. See the
README for details.

Support

New Bug Tracker

While we do our best to respond to questions, feature requests, bug
reports, and other input from users, we must emphasize that PHAST is free,
academic software with no guarantees of support. All requests for support
can be sent by email to
phasthelp@cshl.edu or can be submitted to our
bug tracker and will be addressed in as timely a manner as possible.
Before reporting a bug, please see these
instructions.

Mailing List

Users interested in receiving occasional announcements about PHAST —
advertising new features, new programs, major releases, etc. —
may wish to join the PHAST mailing list. To join, send an email with a blank
subject line and the single word "join" in the message body to
phasthelp@cshl.edu.

Documentation

Funding

PHAST development and maintenance is supported by NIH Grant R01-HG008161.
Past funding sources have included the National Institute of Health (NIH),
the National Science Foundation (NSF), a David and Lucile Packard Fellowship
for Science and Engineerin, an Achievement Rewards for College Scientists (ARCS)
scholarship, and a Graduate Research and Education in Adaptive bio-Technology (GREAT)
fellowship from the University of California Biotechnology Research and
Education Program (UCBREP).